Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.43 kDa 
• Atom Count: 2129 
• Modelled Residue Count: 245 
• Deposited Residue Count: 259 
• Unique protein chains: 2

5L11

Human Liver Receptor Homologue-1 (LRH-1) Bound to RJW100 and a Fragment of TIF-2

• PDB DOI: 10.2210/pdb5L11/pdb

• Classification: transcription/inhibitor
• Organism(s): Homo sapiens
• Expression System: Enterobacteria phage L1
• Mutation(s): No 


• Deposited: 2016-07-28 Released: 2016-10-12 
• Deposition Author(s): Mays, S.G., Ortlund, E.A.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.

Mays, S.G., Okafor, C.D., Whitby, R.J., Goswami, D., Stec, J., Flynn, A.R., Dugan, M.C., Jui, N.T., Griffin, P.R., Ortlund, E.A.

(2016) J Biol Chem 291: 25281-25291

• PubMed: 27694446 
• DOI: 10.1074/jbc.M116.753541
• Primary Citation of Related Structures:  
  5L11, 5SYZ


• PubMed Abstract: 
  

Liver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. Although preclinical and cellular studies demonstrate that LRH-1 has great potential as a therapeutic target for metabolic diseases and cancer, development of LRH-1 modulators has been difficult. Recently, systematic modifications to one of the few known chemical scaffolds capable of activating LRH-1 failed to improve efficacy substantially. Moreover, mechanisms through which LRH-1 is activated by synthetic ligands are entirely unknown. Here, we use x-ray crystallography and other structural methods to explore conformational changes and receptor-ligand interactions associated with LRH-1 activation by a set of related agonists. Unlike phospholipid LRH-1 ligands, these agonists bind deep in the pocket and do not interact with residues near the mouth nor do they expand the pocket like phospholipids. Unexpectedly, two closely related agonists with similar efficacies (GSK8470 and RJW100) exhibit completely different binding modes. The dramatic repositioning is influenced by a differential ability to establish stable face-to-face π-π-stacking with the LRH-1 residue His-390, as well as by a novel polar interaction mediated by the RJW100 hydroxyl group. The differing binding modes result in distinct mechanisms of action for the two agonists. Finally, we identify a network of conserved water molecules near the ligand-binding site that are important for activation by both agonists. This work reveals a previously unappreciated complexity associated with LRH-1 agonist development and offers insights into rational design strategies.

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Organizational Affiliation: 

From the Department of Biochemistry, Emory University School of Medicine, and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 5 group A member 2	A	245	Homo sapiens	Mutation(s): 0  Gene Names: NR5A2, B1F, CPF, FTF
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens) Explore O00482  Go to UniProtKB:  O00482
PHAROS:  O00482 GTEx:  ENSG00000116833

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tif2	B [auth C]	14	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RJW	C [auth A]	(1R,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol C28 H34 O ZFXMYHPLTQTTFW-REUBFRLUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RJW	BindingDB:  5L11	Ki: 374 (nM) from 1 assay(s)
		EC50: min: 251.19, max: 1500 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.418	α = 90
b = 46.418	β = 90
c = 220.259	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-07-28 
• Released Date: 2016-10-12 
Deposition Author(s): Mays, S.G., Ortlund, E.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK095750
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008602
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	F31DK111171

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2016-12-14
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence